Comment[ArrayExpressAccession] E-GEOD-15709
Investigation Title Expression and metylation data from A2780 (cisplatin-sensitive) and Round5 A2780 (cisplatin-resistant) cell lines
Comment[Submitted Name] Expression and metylation data from A2780 (cisplatin-sensitive) and Round5 A2780 (cisplatin-resistant) cell lines
Publication Title Integrated analysis of DNA methylation and gene expression reveals specific signaling pathways associated with platinum resistance in ovarian cancer.
Publication Author List Li M, Balch C, Montgomery JS, Jeong M, Chung JH, Yan P, Huang TH, Kim S, Nephew KP
Publication DOI
PubMed ID 19505326
Experimental Design methylation profiling by array transcription profiling by array
Experimental Design Term Source REF EFO EFO
Public Release Date 2009-04-17
Experiment Description This SuperSeries is composed of the following subset Series: GSE15372: Expression data from A2780 (cisplatin-sensitive) and Round5 A2780 (cisplatin-resistant) cell lines. GSE15373: Promoter CpG island methylation data from A2780 (cisplatin-sensitive) and Round5 A2780 (cisplatin-resistant) cell lines. Refer to individual Series
Date of Experiment
Term Source Name EFO
Term Source Version
Term Source File
Person Last Name Li Li Balch Montgomery Jeong Chung Yan Huang Kim Nephew
Person First Name Meng Meng Curt John Mikyoung JaeHoon Pearlly Tim Sun Kenneth
Person Mid Initials S P
Person Email menli@indiana.edu
Person Affiliation Indiana University
Person Phone
Person Fax
Person Address Medical Sciences, Indiana University, 1001 E 3rd Street, Bloomington, IN, USA
Person Roles submitter
Person Roles Term Source REF
Person Roles Term Accession Number
Normalization Type
Normalization Term Accession Number
Normalization Term Source REF
Replicate Type
Replicate Term Accession Number
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Protocol Name P-GSE15709-11 P-GSE15709-10 P-GSE15709-6 P-GSE15709-4 P-GSE15709-2 P-GSE15709-7 P-GSE15709-1 P-GSE15709-5 P-GSE15709-3 P-GSE15709-9 P-GSE15709-8 P-GSE15709-21 P-GSE15709-16 P-GSE15709-15 P-GSE15709-20 P-GSE15709-18 P-GSE15709-13 P-GSE15709-12 P-GSE15709-14 P-GSE15709-19 P-GSE15709-22 P-GSE15709-17
Protocol Description ID_REF =
VALUE = normalized log2 ratio (Cy5/Cy3) representing test/reference ID_REF =
VALUE = MAS5.0 signal intensity
KN04H010_Detection =
KN04H010_Detection p-value = ID_REF =
VALUE = MAS5.0 signal intensity
KN04H006_Detection =
KN04H006_Detection p-value = ID_REF =
VALUE = MAS5.0 signal intensity
KN04H004_Detection =
KN04H004_Detection p-value = ID_REF =
VALUE = MAS5.0 signal intensity
KN04H002_Detection =
KN04H002_Detection p-value = ID_REF =
VALUE = MAS5.0 signal intensity
KN04H007_Detection =
KN04H007_Detection p-value = ID_REF =
VALUE = MAS5.0 signal intensity
KN04H001_Detection =
KN04H001_Detection p-value = ID_REF =
VALUE = MAS5.0 signal intensity
KN04H005_Detection =
KN04H005_Detection p-value = ID_REF =
VALUE = MAS5.0 signal intensity
KN04H003_Detection =
KN04H003_Detection p-value = ID_REF =
VALUE = MAS5.0 signal intensity
KN04H009_Detection =
KN04H009_Detection p-value = ID_REF =
VALUE = MAS5.0 signal intensity
KN04H008_Detection =
KN04H008_Detection p-value = Scanned on Axon GenePix 4200A scanner (Molecular Devices, Sunnyvale, CA) GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A. Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human U133 plus 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400. Followed Agilent protocol. Genomic DNA was isolated from parental (drug-sensitive) A2780, Round1, Round3, and Round5 cells using Qiagen DNeasy purification kits (Valencia, CA) Trizol extraction of total RNA was performed according to the manufacturer's instructions. Cells were maintained in RPMI 1640 media with 2 mM L-glutamine, 50 U/ml penicillin, 50 mg/ml streptomycin, and 10% fetal bovine serum, at 30o C Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). Labeled the fluorophores Cy3 (parental A2780) or Cy5 (A2780 following various “rounds” of cisplatin treatment) following Agilent protocols LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Data were processed using R program. The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed median target intensity of each array was arbitrarily set to 1000.
Protocol Software
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Protocol Type bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation image_aquisition image_aquisition hybridization hybridization nucleic_acid_extraction nucleic_acid_extraction grow labeling labeling feature_extraction feature_extraction
Protocol Term Source REF
Protocol Term Accession Number
Experimental Factor Name CELL LINE
Experimental Factor Type cell line
Experimental Factor Term Source REF
Experimental Factor Term Accession Number
Comment[SecondaryAccession] GSE15709
Comment[GEOLastUpdateDate] 2009-07-16
Comment[GEOReleaseDate] 2009-04-16
Comment[ArrayExpressSubmissionDate] 2009-04-15
SDRF File E-GEOD-15709.sdrf.txt